DNA is a long threadlike macromolecule comprising a chain of deoxyribonucleotides. Similarly, RNA is composed of a chain of ribonucleotides. A nucleotide consists of a nucleoside, i.e., a nitrogenous base linked to a pentose sugar, and one or more phosphate groups which is usually esterified at the hydroxyl group attached to C-5 of the pentose sugar (indicated as 5') of the nucleoside. Such compounds are called nucleoside 5'-phosphates or 5'-nucleotides. In a molecule of DNA the pentose sugar is deoxyribose, whereas in a molecule of RNA the pentose sugar is ribose. The nitrogenous base can be a purine derivative such as adenine or guanine, or a pyrimidine derivative such as cytosine, thymine (in deoxyribonucleotides) or uracil (in ribonucleotides). Thus, the major nucleotides of DNA are deoxyadenosine 5'-triphosphate (dATP), deoxyguanosine 5'-triphosphate (dGTP), deoxycytidine 5'-triphosphate (dCTP), and deoxythymidine 5'-triphosphate (dTTP). The major nucleotides of RNA are adenosine 5'-triphosphate (ATP), guanosine 5'-triphosphate (GTP), cytidine 5'-triphosphate (CTP) and uridine 5'-triphosphate (UTP).
The sequence of the purine and pyrimidine bases of the DNA or RNA molecule encodes the genetic information contained in the molecule. The sugar and phosphate groups of a DNA or RNA molecule perform a structural role, forming the backbone of the macromolecule. Specifically, the sugar moiety of each nucleotide is linked by a phosphodiester bridge to the sugar moiety of the adjacent nucleotide as follows: the 3'-hydroxyl of the pentose of one nucleotide is joined to the 5'-hydroxyl of the pentose of the adjacent nucleotide by a phosphodiester bond. One terminus of the nucleotide chain has a 5-hydroxyl group and the other terminus of the nucleotide chain has a 3'-hydroxyl group; thus the nucleotide chain has a polarity. By convention, the base sequence of nucleotide chains are written in a 5' to 3' direction.
The formation of the phosphodiester bonds between deoxyribonucleotides is catalyzed by the enzyme DNA polymerase. DNA polymerase requires the following components to catalyze the synthesis of a chain of DNA: a template strand (e.g. a single-stranded DNA molecule), a primer (i.e., a short DNA or RNA chain with a free 3'-hydroxyl group, that is hybridized to a specific site on the single-stranded template), and activated deoxyribonucleotide precursors (i.e., nucleoside 5'-triphosphates or dNTPs). Elongation of the primer strand, catalyzed by DNA polymerase, proceeds in the 5' to 3' direction along the template. The occurs by means of nucleophilic attack of the 3'-hydroxyl terminus of the primer on the innermost phosphorous atom of the incoming nucleotide; a phosphodiester bridge is formed and pyrophosphate is released. DNA polymerase catalyzes the formation of a phosphodiester bond only if the base of the incoming nucleotide is complementary to the base of the nucleotide on the template strand; that is, the incoming nucleotide must form the correct Watson-Crick type of basepair with the template. Thus, DNA polymerase is a template-directed enzyme. Reverse transcriptase is also a template-directed DNA polymerase, but requires RNA as its template. Another enzyme, RNA polymerase, catalyzes the polymerization of activated ribonucleotide precursors that are complementary to the DNA template. Some polymerases, such as E.coli DNA polymerase I and T4 DNA polymerase, also have a 3' to 5' exonuclease activity that acts on unpaired termini. This 3' to 5' exonuclease activity serves a "proof-reading" function by removing mispaired bases before polymerization continues; i.e., the mispaired bases are edited out of the elongating strand.